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- PDB-2uzp: Crystal structure of the C2 domain of human protein kinase C gamma. -

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Basic information

Entry
Database: PDB / ID: 2uzp
TitleCrystal structure of the C2 domain of human protein kinase C gamma.
ComponentsPROTEIN KINASE C GAMMA TYPE
KeywordsTRANSFERASE / METAL-BINDING / KINASE / ZINC-FINGER / ATP-BINDING / SPINOCEREBELLAR ATAXIA / CALCIUM-BINDING PROTEIN / SERINE/THREONINE-PROTEIN KINASE / PHOSPHOLIPID BINDING PROTEIN / NUCLEOTIDE-BINDING / PHORBOL- ESTER BINDING / PHOSPHORYLATION / PROTEIN KINASE C / NEURODEGENERATION
Function / homology
Function and homology information


Disinhibition of SNARE formation / Response to elevated platelet cytosolic Ca2+ / regulation of response to food / calcium,diacylglycerol-dependent serine/threonine kinase activity / positive regulation of mismatch repair / Trafficking of GluR2-containing AMPA receptors / WNT5A-dependent internalization of FZD4 / protein kinase C / chemosensory behavior / negative regulation of proteasomal protein catabolic process ...Disinhibition of SNARE formation / Response to elevated platelet cytosolic Ca2+ / regulation of response to food / calcium,diacylglycerol-dependent serine/threonine kinase activity / positive regulation of mismatch repair / Trafficking of GluR2-containing AMPA receptors / WNT5A-dependent internalization of FZD4 / protein kinase C / chemosensory behavior / negative regulation of proteasomal protein catabolic process / diacylglycerol-dependent serine/threonine kinase activity / innervation / regulation of phagocytosis / presynaptic cytosol / response to morphine / Calmodulin induced events / postsynaptic cytosol / response to psychosocial stress / regulation of synaptic vesicle exocytosis / response to pain / calyx of Held / negative regulation of protein ubiquitination / presynaptic modulation of chemical synaptic transmission / protein serine/threonine/tyrosine kinase activity / synaptic membrane / long-term synaptic potentiation / regulation of circadian rhythm / negative regulation of protein catabolic process / response to toxic substance / G alpha (z) signalling events / cell-cell junction / rhythmic process / chemical synaptic transmission / negative regulation of neuron apoptotic process / postsynaptic density / learning or memory / protein kinase activity / intracellular signal transduction / phosphorylation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / dendrite / perinuclear region of cytoplasm / zinc ion binding / ATP binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Protein kinase C, alpha/beta/gamma types / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding / C2 domain / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / C2 domain / Protein kinase C conserved region 2 (CalB) / Zinc finger phorbol-ester/DAG-type profile. ...Protein kinase C, alpha/beta/gamma types / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding / C2 domain / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / C2 domain / Protein kinase C conserved region 2 (CalB) / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C2 domain / C2 domain profile. / C1-like domain superfamily / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / C2 domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / PYRIDOXAL-5'-PHOSPHATE / Protein kinase C gamma type
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPike, A.C.W. / Amos, A. / Johansson, C. / Sobott, F. / Savitsky, P. / Berridge, G. / Fedorov, O. / Umeano, C. / Gorrec, F. / Bunkoczi, G. ...Pike, A.C.W. / Amos, A. / Johansson, C. / Sobott, F. / Savitsky, P. / Berridge, G. / Fedorov, O. / Umeano, C. / Gorrec, F. / Bunkoczi, G. / Debreczeni, J. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Weigelt, J. / Sundstrom, M. / Knapp, S.
CitationJournal: To be Published
Title: Crystal Structure of C2 Domain of Protein Kinase C Gamma
Authors: Pike, A.C.W. / Amos, A. / Johansson, C. / Sobott, F. / Savitsky, P. / Berridge, G. / Fedorov, O. / Umeano, C. / Gorrec, F. / Bunkoczi, G. / Debreczeni, J. / von Delft, F. / Arrowsmith, C.H. ...Authors: Pike, A.C.W. / Amos, A. / Johansson, C. / Sobott, F. / Savitsky, P. / Berridge, G. / Fedorov, O. / Umeano, C. / Gorrec, F. / Bunkoczi, G. / Debreczeni, J. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Weigelt, J. / Sundstrom, M. / Knapp, S.
History
DepositionApr 30, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 19, 2014Group: Advisory / Atomic model ...Advisory / Atomic model / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN KINASE C GAMMA TYPE
B: PROTEIN KINASE C GAMMA TYPE
C: PROTEIN KINASE C GAMMA TYPE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,29846
Polymers49,6013
Non-polymers3,69743
Water7,062392
1
A: PROTEIN KINASE C GAMMA TYPE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,66014
Polymers16,5341
Non-polymers1,12713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PROTEIN KINASE C GAMMA TYPE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,75715
Polymers16,5341
Non-polymers1,22314
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: PROTEIN KINASE C GAMMA TYPE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,88117
Polymers16,5341
Non-polymers1,34716
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)138.503, 138.503, 68.358
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.85791, -0.51344, 0.01933), (-0.51376, 0.85773, -0.01872), (-0.00697, -0.02599, -0.99964)94.86041, 26.73574, 69.39318
2given(-0.4881, -0.8724, 0.02602), (0.87265, -0.48834, -0.00347), (0.01574, 0.02101, 0.99966)94.37377, 25.1976, -1.23206

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein PROTEIN KINASE C GAMMA TYPE / PROTEIN KINASE C GAMMA / PKC-GAMMA


Mass: 16533.654 Da / Num. of mol.: 3 / Fragment: C2 DOMAIN, RESIDUES 154-295
Source method: isolated from a genetically manipulated source
Details: SCHIFFS BASE LINK BETWEEN SER -1 AND PYRIDOXAL PHOSPHATE PLP300
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P05129, protein kinase C

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Non-polymers , 6 types, 435 molecules

#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Co
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsN-TERMINAL SER MET ARISE FROM VECTOR-ENCODED PROTEASE RECOGNITION SEQUENCE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.31 Å3/Da / Density % sol: 62.88 %
Crystal growpH: 6.5
Details: 1.8M AMMONIUM SULPHATE, 15MM COBALT CHLORIDE, 0.1M MES PH6.5, pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 18, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2→56.08 Å / Num. obs: 45478 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 10.2 % / Biso Wilson estimate: 28.17 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.7
Reflection shellResolution: 2→2.11 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 3.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DSY

1dsy


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.117 / SU ML: 0.088 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. AMINO TERMINUS IS MODIFIED BY PYRIXODAL PHOSPHATE DURING CRYSTALLIZATION AND TIGHTLY COORDINATES A COBALT ION
RfactorNum. reflection% reflectionSelection details
Rfree0.205 2295 5 %RANDOM
Rwork0.171 ---
obs0.172 43180 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.14 Å2
Baniso -1Baniso -2Baniso -3
1--1.01 Å20 Å20 Å2
2---1.01 Å20 Å2
3---2.03 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3410 0 189 392 3991
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223750
X-RAY DIFFRACTIONr_bond_other_d0.0020.022541
X-RAY DIFFRACTIONr_angle_refined_deg1.3132.0085084
X-RAY DIFFRACTIONr_angle_other_deg0.84736159
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6475434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.54423.829175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.53615607
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.321533
X-RAY DIFFRACTIONr_chiral_restr0.0760.2530
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023978
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02715
X-RAY DIFFRACTIONr_nbd_refined0.1960.2617
X-RAY DIFFRACTIONr_nbd_other0.1990.22734
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21637
X-RAY DIFFRACTIONr_nbtor_other0.0940.21962
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2289
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2440.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1990.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.40132274
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.07253539
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.31181710
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.114111543
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.268 189
Rwork0.214 3121
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.78130.55640.62881.80190.88261.2168-0.01140.0789-0.152-0.1544-0.0155-0.01390.07670.01170.0268-0.1847-0.02010.0051-0.23010.0101-0.030437.04818.84219.944
23.0040.28430.58921.6545-0.04931.9711-0.005-0.3973-0.40860.3587-0.0476-0.42120.23510.26410.0526-0.12270.0372-0.0863-0.12930.13250.046253.45723.8948.64
32.3375-0.4402-0.411.2660.19361.59630.00380.3160.1492-0.23110.0271-0.208-0.10180.2206-0.0308-0.1984-0.0633-0.0071-0.14870.0769-0.027160.38448.22819.77
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 293
2X-RAY DIFFRACTION2B-1 - 293
3X-RAY DIFFRACTION3C-1 - 293

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